11th June 2020
#Import libraries needed for data analysis and plotting
suppressPackageStartupMessages({
library(rtracklayer)
library(optparse)
library(GenomicRanges)
library(gridExtra)
library(DESeq2)
library(umap)
library(BRGenomics)
library(tidyverse)
library(viridis)
library(ggpointdensity)
});
options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=3, repr.plot.height=2);
#1. Import coordinates of maxTSS in K562:
#Read in enhancers and promtoers maxTSS
promoters.maxTSS = read.table("/local/storage/data/hg19/k562/copro/promoter.maxTSS.K562.bed", header = T);
enhancers.maxTSS = read.table("/local/storage/data/hg19/k562/copro/enhancers.maxTSS.K562.bed", header = T);
#Convert them to GRanges
promoters.maxTSS = makeGRangesFromDataFrame(promoters.maxTSS);
enhancers.maxTSS = makeGRangesFromDataFrame(enhancers.maxTSS);
#Resize them to 4kb: each entries consists of the base-start positions of each maxTSS
promoters.maxTSS = promoters(promoters.maxTSS, upstream=2000, downstream=2000);
enhancers.maxTSS = promoters(enhancers.maxTSS, upstream=2000, downstream=2000);
(promoters.maxTSS)
GRanges object with 11462 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr6 27858964-27862963 -
[2] chr19 47727531-47731530 +
[3] chr7 26238367-26242366 -
[4] chr6 27112885-27116884 +
[5] chr11 65264516-65268515 +
... ... ... ...
[11458] chr20 62166820-62170819 +
[11459] chr21 42790562-42794561 +
[11460] chr22 37606696-37610695 +
[11461] chr22 45403975-45407974 +
[11462] chrX 86770793-86774792 +
-------
seqinfo: 23 sequences from an unspecified genome; no seqlengths
all.TSS = append(promoters.maxTSS, enhancers.maxTSS);
all.TSS
GRanges object with 26340 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr6 27858964-27862963 -
[2] chr19 47727531-47731530 +
[3] chr7 26238367-26242366 -
[4] chr6 27112885-27116884 +
[5] chr11 65264516-65268515 +
... ... ... ...
[26336] chrX 106394425-106398424 +
[26337] chrX 129215275-129219274 +
[26338] chrX 131136963-131140962 +
[26339] chrX 151155950-151159949 +
[26340] chrX 152542098-152546097 +
-------
seqinfo: 23 sequences from an unspecified genome; no seqlengths
#1. Import gene coordinates in hg19
genes=read.table("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/gencode.v19.annotation.gtf.gz", header=F, stringsAsFactors=F);
colnames(genes) = c("chr", "Transcript", "start", "end", "strand", "gene_id", "transcript_id", "gene_type", "gene_name", "TranscriptName");
genes = genes[genes$Transcript =="transcript",];
genes = as(genes, "GRanges");
#Order genes based on their length
genes = genes[order(width(genes))];
genes = genes[!duplicated(genes$gene_name)];
genes = genes[width(genes) > 250];
genes_resize = promoters(genes, upstream=2000, downstream=2000);
genes_resize
GRanges object with 19438 ranges and 6 metadata columns:
seqnames ranges strand | Transcript gene_id
<Rle> <IRanges> <Rle> | <character> <character>
41040 chr1 26211851-26215850 + | transcript ENSG00000229786.1
398133 chr2 216667705-216671704 - | transcript ENSG00000216721.3
827754 chr6 29943244-29947243 + | transcript ENSG00000204625.6
98756 chr1 73655539-73659538 - | transcript ENSG00000251825.1
114834 chr1 100562795-100566794 + | transcript ENSG00000226952.1
... ... ... ... . ... ...
548232 chr3 139652029-139656028 + | transcript ENSG00000158258.11
488244 chr3 50710672-50714671 + | transcript ENSG00000088538.12
282161 chr2 60325336-60329335 - | transcript ENSG00000271955.1
924687 chr6 163146797-163150796 - | transcript ENSG00000185345.14
278270 chr2 51257739-51261738 + | transcript ENSG00000231918.1
transcript_id gene_type gene_name TranscriptName
<character> <character> <character> <character>
41040 ENST00000440710.1 pseudogene SNRPFP2 SNRPFP2-001
398133 ENST00000454121.1 pseudogene AC093850.1 AC093850.1-001
827754 ENST00000463275.1 lincRNA HCG9 HCG9-002
98756 ENST00000516016.1 misc_RNA RN7SKP19 RN7SKP19-201
114834 ENST00000443135.1 pseudogene RP4-714D9.4 RP4-714D9.4-001
... ... ... ... ...
548232 ENST00000511524.1 protein_coding CLSTN2 CLSTN2-002
488244 ENST00000266037.9 protein_coding DOCK3 DOCK3-001
282161 ENST00000606382.1 lincRNA RP11-444A22.1 RP11-444A22.1-001
924687 ENST00000366892.1 protein_coding PARK2 PARK2-002
278270 ENST00000440698.1 lincRNA AC007682.1 AC007682.1-001
-------
seqinfo: 7 sequences from an unspecified genome; no seqlengths
#1. Import H3K36me3 and WCE BAMs (as Rdata)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_0h_br1.Rdata");
K4me3_0h_br1 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_1h_br1.Rdata");
K4me3_1h_br1 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_4h_br1.Rdata");
K4me3_4h_br1 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_0h_br2.Rdata");
K4me3_0h_br2 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_1h_br2.Rdata");
K4me3_1h_br2 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_4h_br2.Rdata");
K4me3_4h_br2 = reads;
rm(reads)
#WCE
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_0h_br1_JJO19.Rdata");
WCE_0h_br1 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_1h_br1_JJO19.Rdata");
WCE_1h_br1 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_4h_br1_JJO19.Rdata");
WCE_4h_br1 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_0h_br2_JJO19.Rdata");
WCE_0h_br2 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_1h_br2_JJO19.Rdata");
WCE_1h_br2 = reads;
rm(reads)
load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_4h_br2_JJO19.Rdata");
WCE_4h_br2 = reads;
rm(reads)
Count.reads.InBins = function(mark.BAM, regions, spike = 1, binsize = 1, field = "score"){
#Resize each read from BAM to 1bp (center position of each read)
mark.BAM.res = resize(mark.BAM, width = 1, fix = "center");
#Compute coverage
mark.BAM.res = GRanges(coverage(mark.BAM.res, weight="count"));
mark.BAM.res = makeGRangesBRG(mark.BAM.res[mark.BAM.res$score > 0]);
#Count DHS signal within each CTCF peak
mark.BAM.score = getCountsByPositions(mark.BAM.res, regions, binsize = binsize, field="score");
return(mark.BAM.score/spike)
}
#4. Experimental H3K36me3 signal in regions of interest
K4me3_0h_br1.perBin = Count.reads.InBins(K4me3_0h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
K4me3_1h_br1.perBin = Count.reads.InBins(K4me3_1h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
K4me3_4h_br1.perBin = Count.reads.InBins(K4me3_4h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
K4me3_0h_br2.perBin = Count.reads.InBins(K4me3_0h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
K4me3_1h_br2.perBin = Count.reads.InBins(K4me3_1h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
K4me3_4h_br2.perBin = Count.reads.InBins(K4me3_4h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
#5. WCE reads in regions of interest
WCE.K27ac_0h_br1.perBin = Count.reads.InBins(WCE_0h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
WCE.K27ac_1h_br1.perBin = Count.reads.InBins(WCE_1h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
WCE.K27ac_4h_br1.perBin = Count.reads.InBins(WCE_4h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
WCE.K27ac_0h_br2.perBin = Count.reads.InBins(WCE_0h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
WCE.K27ac_1h_br2.perBin = Count.reads.InBins(WCE_1h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
WCE.K27ac_4h_br2.perBin = Count.reads.InBins(WCE_4h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
#6. Calculate theotic value from the linear regressions and the WCE reads per Bin
K4me3_0h_br1.theoretic.perBin = (0.96111 * WCE.K27ac_0h_br1.perBin) + 27.42451;
K4me3_1h_br1.theoretic.perBin = (0.11971 * WCE.K27ac_1h_br1.perBin) + 6.64561;
K4me3_4h_br1.theoretic.perBin = (0.44505 * WCE.K27ac_4h_br1.perBin) + 12.22014;
K4me3_0h_br2.theoretic.perBin = (0.34377 * WCE.K27ac_0h_br2.perBin) + 13.10884;
K4me3_1h_br2.theoretic.perBin = (0.25230 * WCE.K27ac_1h_br2.perBin) + 10.46680;
K4me3_4h_br2.theoretic.perBin = (0.21612 * WCE.K27ac_4h_br2.perBin) + 3.01524;
#7. Calculate the residuals
res_0h_br1 = K4me3_0h_br1.perBin - K4me3_0h_br1.theoretic.perBin;
res_1h_br1 = K4me3_1h_br1.perBin - K4me3_1h_br1.theoretic.perBin;
res_4h_br1 = K4me3_4h_br1.perBin - K4me3_4h_br1.theoretic.perBin;
res_0h_br2 = K4me3_0h_br2.perBin - K4me3_0h_br2.theoretic.perBin;
res_1h_br2 = K4me3_1h_br2.perBin - K4me3_1h_br2.theoretic.perBin;
res_4h_br2 = K4me3_4h_br2.perBin - K4me3_4h_br2.theoretic.perBin;
#8. Replace all residuals < 0 with 0
res_0h_br1[res_0h_br1 < 0] = 0;
res_1h_br1[res_1h_br1 < 0] = 0;
res_4h_br1[res_4h_br1 < 0] = 0;
res_0h_br2[res_0h_br2 < 0] = 0;
res_1h_br2[res_1h_br2 < 0] = 0;
res_4h_br2[res_4h_br2 < 0] = 0;
#9. Keep only the entries were both replicates have reads
badgenes_0h = which(rowSums(res_0h_br1)<1 | rowSums(res_0h_br2)<1 | rowSums(res_1h_br1)<1 | rowSums(res_1h_br2)<1 | rowSums(res_4h_br1)<1 | rowSums(res_4h_br2)<1);
filtered_0h_br1 = res_0h_br1[-badgenes_0h,];
filtered_0h_br2 = res_0h_br2[-badgenes_0h,];
#1h
filtered_1h_br1 = res_1h_br1[-badgenes_0h,];
filtered_1h_br2 = res_1h_br2[-badgenes_0h,];
#4h
filtered_4h_br1 = res_4h_br1[-badgenes_0h,];
filtered_4h_br2 = res_4h_br2[-badgenes_0h,];
length(filtered_0h_br1)
#9. Subsample residual matrices and plot metaplots
res_0h_br1.subs = metaSubsampleMatrix(filtered_0h_br1 /2530);
res_1h_br1.subs = metaSubsampleMatrix(filtered_1h_br1 /3048);
res_4h_br1.subs = metaSubsampleMatrix(filtered_4h_br1 /4108);
res_0h_br2.subs = metaSubsampleMatrix(filtered_0h_br2 /346 * 0.267234624149712);
res_1h_br2.subs = metaSubsampleMatrix(filtered_1h_br2 /1724 * 0.267234624149712);
res_4h_br2.subs = metaSubsampleMatrix(filtered_4h_br2 /1782 * 0.267234624149712);
#10. Give miningful names to each dataset --> thse names will be used as labels for the plot
res_0h_br1.subs$sample.name = "0h Rep1";
res_1h_br1.subs$sample.name = "1h Rep1";
res_4h_br1.subs$sample.name = "4h Rep1";
res_0h_br2.subs$sample.name = "0h Rep2";
res_1h_br2.subs$sample.name = "1h Rep2";
res_4h_br2.subs$sample.name = "4h Rep2";
theme_set(
theme_classic() +
theme(
panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=0.5),
panel.grid.major = element_line(colour = "white"),
axis.text.x = element_text( color="black", size=14),
axis.text.y = element_text( color="black", size=16),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=16)
)
);
####All gencode annotated genes
#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles
# ----> Promoters
plot_BR1.RPM = rbind(res_0h_br1.subs, res_1h_br1.subs, res_4h_br1.subs);
ggplot(plot_BR1.RPM, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
#title = "\n H3K4me3 promoters - Replicate 1 \n ",
x = "Distance from TSS [kb]",
y = "Normalized \n signal"
)
plot_BR2.RPM = rbind(res_0h_br2.subs, res_1h_br2.subs, res_4h_br2.subs);
ggplot(plot_BR2.RPM, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
#title = "\n H3K4me3 promoters - Replicate 2 \n ",
x = "Distance from TSS [kb]",
y = "Normalized \n signal"
)
####All gencode annotated genes
#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles
# ----> Promoters
plot_BR1.RPM = rbind(res_0h_br1.subs, res_1h_br1.subs, res_4h_br1.subs);
ggplot(plot_BR1.RPM, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
#title = "\n H3K4me3 promoters - Replicate 1 \n ",
x = "Distance from TSS [kb]",
y = "Normalized \n signal"
)
plot_BR2.RPM = rbind(res_0h_br2.subs, res_1h_br2.subs, res_4h_br2.subs);
ggplot(plot_BR2.RPM, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
#title = "\n H3K4me3 promoters - Replicate 2 \n ",
x = "Distance from TSS [kb]",
y = "Normalized \n signal"
)
#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles
# ----> Promoters
plot_BR1.RPM = rbind(res_0h_br1.subs, res_1h_br1.subs, res_4h_br1.subs);
ggplot(plot_BR1.RPM, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
#title = "\n H3K4me3 promoters - Replicate 1 \n ",
x = "Distance from TSS [kb]",
y = "Normalized \n signal"
)
plot_BR2.RPM = rbind(res_0h_br2.subs, res_1h_br2.subs, res_4h_br2.subs);
ggplot(plot_BR2.RPM, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
#title = "\n H3K4me3 promoters - Replicate 2 \n ",
x = "Distance from TSS [kb]",
y = "Normalized \n signal"
)
sum(res_0h_br1.subs$mean)/sum(res_0h_br2.subs$mean)
#Remove top and bottom 2.5% of data for K-S tests
#rSums_0h_br1 = rowSums(filtered_0h_br1)[round(0.025*length(rowSums(filtered_0h_br1))):round(0.975* length(rowSums(filtered_0h_br1)))]/3002;
#rSums_1h_br1 = rowSums(filtered_1h_br1)[round(0.025*length(rowSums(filtered_1h_br1))):round(0.975* length(rowSums(filtered_1h_br1)))]/9218;
#rSums_4h_br1 = rowSums(filtered_4h_br1)[round(0.025*length(rowSums(filtered_4h_br1))):round(0.975* length(rowSums(filtered_4h_br1)))]/8084;
#Rep 2:
#rSums_0h_br2 = rowSums(filtered_0h_br2)[round(0.025*length(rowSums(filtered_0h_br2))):round(0.975* length(rowSums(filtered_0h_br2)))]/1042 * 0.673771984137532;
#rSums_1h_br2 = rowSums(filtered_1h_br2)[round(0.025*length(rowSums(filtered_1h_br2))):round(0.975* length(rowSums(filtered_1h_br2)))]/7368 * 0.673771984137532;
#rSums_4h_br2 = rowSums(filtered_4h_br2)[round(0.025*length(rowSums(filtered_4h_br2))):round(0.975* length(rowSums(filtered_4h_br2)))]/7984 * 0.673771984137532;
rSums_0h_br1 = rowSums(filtered_0h_br1)/2530;
rSums_1h_br1 = rowSums(filtered_1h_br1)/3048;
rSums_4h_br1 = rowSums(filtered_4h_br1)/4108;
rSums_0h_br2 = rowSums(filtered_0h_br2)/346 * 0.267234624149712;
rSums_1h_br2 = rowSums(filtered_1h_br2)/1724 * 0.267234624149712;
rSums_4h_br2 = rowSums(filtered_4h_br2)/1782 * 0.267234624149712;
#Left merge the 2 peaks (knowing that they have the same peak.name column, in the same order)
# 0h
mark_0h = cbind((rSums_0h_br1), (rSums_0h_br2));
colnames(mark_0h) = c("Rep1", "Rep2");
# 1h
mark_1h = cbind((rSums_1h_br1), (rSums_1h_br2));
colnames(mark_1h) = c("Rep1", "Rep2");
# 4h
mark_4h = cbind((rSums_4h_br1), (rSums_4h_br2));
colnames(mark_4h) = c("Rep1", "Rep2");
### VII. Plot and correlate 0h datasets
#For correlations can also use:
cor.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"], method = "pearson");
cor.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"], method = "spearman");
Pearson's product-moment correlation
data: mark_0h[, "Rep1"] and mark_0h[, "Rep2"]
t = 448.13, df = 9250, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.9768202 0.9786155
sample estimates:
cor
0.9777357
Warning message in cor.test.default(mark_0h[, "Rep1"], mark_0h[, "Rep2"], method = "spearman"): "Cannot compute exact p-value with ties"
Spearman's rank correlation rho
data: mark_0h[, "Rep1"] and mark_0h[, "Rep2"]
S = 4211065336, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.9680966
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(mark_0h), mapping=aes(Rep2, Rep1)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 - 4kb around promoter TSSs \n P = 0.9787136, S = 0.9707956 \n",
x = "Rep II 0h",
y = "Rep I 0h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
### VII. Plot and correlate 0h datasets
#For correlations can also use:
cor.test(mark_1h[, "Rep1"], mark_1h[, "Rep2"], method = "pearson");
cor.test(mark_1h[, "Rep1"], mark_1h[, "Rep2"], method = "spearman");
Pearson's product-moment correlation
data: mark_1h[, "Rep1"] and mark_1h[, "Rep2"]
t = 183.95, df = 9839, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.8756541 0.8845588
sample estimates:
cor
0.8801839
Spearman's rank correlation rho
data: mark_1h[, "Rep1"] and mark_1h[, "Rep2"]
S = 2.0899e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.8684296
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(mark_1h), mapping=aes(Rep2, Rep1)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 - 4kb around promoter TSSs \n P = 0.8801839, S = 0.8684298 \n",
x = "Rep II 1h",
y = "Rep I 1h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
### VII. Plot and correlate 0h datasets
#For correlations can also use:
cor.test(mark_4h[, "Rep1"], mark_4h[, "Rep2"], method = "pearson");
cor.test(mark_4h[, "Rep1"], mark_4h[, "Rep2"], method = "spearman");
Pearson's product-moment correlation
data: mark_4h[, "Rep1"] and mark_4h[, "Rep2"]
t = 170.59, df = 9839, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.8594043 0.8693915
sample estimates:
cor
0.8644832
Spearman's rank correlation rho
data: mark_4h[, "Rep1"] and mark_4h[, "Rep2"]
S = 2.3863e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.8497667
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(mark_4h), mapping=aes(Rep2, Rep1)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 - 4kb around promoter TSSs \n P = 0.8644832, S = 0.8497667 \n",
x = "Rep II 4h",
y = "Rep I 4h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
ks.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"]);
Warning message in ks.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"]): "p-value will be approximate in the presence of ties"
Two-sample Kolmogorov-Smirnov test data: mark_0h[, "Rep1"] and mark_0h[, "Rep2"] D = 0.035452, p-value = 1.782e-05 alternative hypothesis: two-sided
#Plot the samples together
x = append(mark_0h[, "Rep1"], mark_0h[, "Rep2"]);
lab = gl(2, length(mark_0h[, "Rep1"]), labels = c("0h_br1", "0h_br2"));
ggplot(as.data.frame(cbind(x, lab)), aes(x=as.numeric(x), group = as.numeric(lab), col=lab)) + stat_ecdf(geom = "point") +
scale_x_log10() +
labs(
title = "\n K-S test: 0h Rep1 vs 0h Rep2 \n D = 0.035057 \n",
x = " Log Residual H3K4me3 1h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=28, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=24, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
ks.test(mark_1h[, "Rep1"], mark_1h[, "Rep2"]);
Two-sample Kolmogorov-Smirnov test data: mark_1h[, "Rep1"] and mark_1h[, "Rep2"] D = 0.42191, p-value < 2.2e-16 alternative hypothesis: two-sided
#Plot the samples together
x = append(mark_1h[, "Rep1"], mark_1h[, "Rep2"]);
lab = gl(2, length(mark_1h[, "Rep1"]), labels = c("1h_br1", "1h_br2"));
ggplot(as.data.frame(cbind(x, lab)), aes(x=as.numeric(x), group = as.numeric(lab), col=lab)) + stat_ecdf(geom = "point") +
scale_x_log10() +
labs(
title = "\n K-S test: 1h Rep1 vs 0h Rep2 \n D = 0.42191 \n",
x = " Log Residual H3K4me3 1h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=28, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=24, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
ks.test(mark_4h[, "Rep1"], mark_4h[, "Rep2"]);
Two-sample Kolmogorov-Smirnov test data: mark_4h[, "Rep1"] and mark_4h[, "Rep2"] D = 0.48765, p-value < 2.2e-16 alternative hypothesis: two-sided
#Plot the samples together
x = append(mark_4h[, "Rep1"], mark_4h[, "Rep2"]);
lab = gl(2, length(mark_4h[, "Rep1"]), labels = c("4h_br1", "4h_br2"));
ggplot(as.data.frame(cbind(x, lab)), aes(x=as.numeric(x), group = as.numeric(lab), col=lab)) + stat_ecdf(geom = "point") +
scale_x_log10() +
labs(
title = "\n K-S test: 4h Rep1 vs 0h Rep2 \n D = 0.48765 \n",
x = " Log Residual H3K4me3 4h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=28, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=24, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
Draw Violin plots to show the distribution of normalized H3K4me3 signal at promoters¶library(tidyverse)
mark_violin = tibble(
R1_0h=mark_0h[, "Rep1"],
R2_0h=mark_0h[, "Rep2"],
R1_1h=mark_1h[, "Rep1"],
R2_1h=mark_1h[, "Rep2"],
R1_4h=mark_4h[, "Rep1"],
R2_4h=mark_4h[, "Rep2"],
ID = 1:length(R1_0h)
) %>%
pivot_longer( R1_0h:R2_4h, names_to = "Sample", values_to = "Signal" ) %>%
#substr = select from column "Sample" at start=2, end=2
mutate( Rep=substr(Sample, 2, 2), time=substr(Sample, 4, 5) );
# ---> Promoters
ggplot(mark_violin, aes(x=paste0(time, Rep), y=as.numeric(Signal), col=time)) +
geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F ) +
scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
labs(
x = "",
y = "Log normalized"
) +
scale_x_discrete()
Warning message: "Transformation introduced infinite values in continuous y-axis" Warning message: "Removed 402 rows containing non-finite values (stat_ydensity)."
ggplot(mark_violin, aes(x=paste0(time, Rep), y=as.numeric(Signal), col=time)) +
geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F) +
scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_log10() +
labs(
x = "",
y = "Relative signal"
) +
scale_x_discrete()
Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.
Draw PCA for normalized H3K4me3 signal within peaks¶#1. Merge all signals per peaks into one signle matrix
mark_PCA = cbind(as.numeric(mark_0h[, "Rep1"]), as.numeric(mark_1h[, "Rep1"]),
as.numeric(mark_4h[, "Rep1"]), as.numeric(mark_0h[, "Rep2"]),
as.numeric(mark_1h[, "Rep2"]), as.numeric(mark_4h[, "Rep2"]));
colnames(mark_PCA) = c("H3K4me3 0h BR1", "H3K4me3 1h BR1", "H3K4me3 4h BR1", "H3K27H3K4me3c 0h BR2", "H3K4me3 1h BR2", "H3K4me3 4h BR2");
#If any, replace all NAs with 0
mark_PCA[is.na(mark_PCA)] = 0;
head(mark_PCA)
| H3K4me3 0h BR1 | H3K4me3 1h BR1 | H3K4me3 4h BR1 | H3K27H3K4me3c 0h BR2 | H3K4me3 1h BR2 | H3K4me3 4h BR2 |
|---|---|---|---|---|---|
| 0.8105001 | 0.08513178 | 0.15229185 | 0.6295785 | 0.08982861 | 0.1633068 |
| 0.5552439 | 0.06959867 | 0.10917628 | 0.4821538 | 0.04467459 | 0.1135402 |
| 0.5368228 | 0.07509226 | 0.08996878 | 0.3989542 | 0.07055816 | 0.1213926 |
| 0.3906044 | 0.06263347 | 0.09843864 | 0.3276587 | 0.03615007 | 0.0834512 |
| 0.3628903 | 0.03356353 | 0.07138911 | 0.3400055 | 0.04185720 | 0.1108769 |
| 0.6122549 | 0.08207975 | 0.09343375 | 0.4286424 | 0.07611265 | 0.1291515 |
#Make PCA:
options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=7, repr.plot.height=8);
cols <- rep(1:2, each=3);
pch <- c(rep(c(1:3),2));
legend <- colnames(mark_PCA);
pc.cr <- princomp(mark_PCA, cor = TRUE)
pairs(pc.cr$loadings[, 1:5], col=cols, pch=pch)
#legend("bottomleft", pch=c(1:3), legend=colnames(K27ac_PCA))
summary(pc.cr)
Importance of components:
Comp.1 Comp.2 Comp.3 Comp.4 Comp.5
Standard deviation 2.3669389 0.51225802 0.235219719 0.208576470 0.157429772
Proportion of Variance 0.9337333 0.04373471 0.009221386 0.007250691 0.004130689
Cumulative Proportion 0.9337333 0.97746798 0.986689361 0.993940052 0.998070741
Comp.6
Standard deviation 0.107589761
Proportion of Variance 0.001929259
Cumulative Proportion 1.000000000
#1. Average normalized replicates
filtered_0h = ((res_0h_br1 /2530) + (res_0h_br2 /346))/2;
filtered_1h = ((res_1h_br1 /3048) + (res_1h_br2 /1724))/2;
filtered_4h = ((res_4h_br1 /4108) + (res_4h_br2 /1782))/2;
#write.table(rowSums(filtered_0h), "./K4me3.allTSS.4kb_0h_ReadyForPlotting.bed", quote=F, sep="\t", row.names=F, col.names=F);
#write.table(rowSums(filtered_1h), "./K4me3.allTSS.4kb_1h_ReadyForPlotting.bed", quote=F, sep="\t", row.names=F, col.names=F);
#write.table(rowSums(filtered_4h), "./K4me3.allTSS.4kb_4h_ReadyForPlotting.bed", quote=F, sep="\t", row.names=F, col.names=F);
#9. Subsample residual matrices and plot metaplots
res_0h.subs = metaSubsampleMatrix(filtered_0h);
res_1h.subs = metaSubsampleMatrix(filtered_1h);
res_4h.subs = metaSubsampleMatrix(filtered_4h);
#10. Give miningful names to each dataset --> thse names will be used as labels for the plot
res_0h.subs$sample.name = "0h ";
res_1h.subs$sample.name = "1h ";
res_4h.subs$sample.name = "4h ";
theme_set(
theme_classic() +
theme(
panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=0.5),
panel.grid.major = element_line(colour = "white"),
axis.text.x = element_text( color="black", size=14),
axis.text.y = element_text( color="black", size=16),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=16)
)
);
#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles ---> RPM norm data
# --> Enhancers
options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=3, repr.plot.height=2);
plot.merged = rbind(res_0h.subs, res_1h.subs, res_4h.subs);
ggplot(plot.merged, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
#scale_colour_manual(values = c("#005ab3", "#ff8da1", "#ff6500")) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 2, 4), breaks=c(0.00, 0.02, 0.04)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
x = " Distance to TSS [kb]",
y = "Normalized \n signal "
)
Draw Violin plots to show the distribution of normalized H3K4me3 signal at promoters¶mark_violin = tibble(
R1_0h=rowSums(filtered_0h),
R1_1h=rowSums(filtered_1h),
R1_4h=rowSums(filtered_4h),
ID = 1:length(R1_0h)
) %>%
pivot_longer( R1_0h:R1_4h, names_to = "Sample", values_to = "Signal" ) %>%
#substr = select from column "Sample" at start=2, end=2
mutate( Rep=substr(Sample, 2, 2), time=substr(Sample, 4, 5) );
ggplot(mark_violin, aes(x=paste0(time, " "), y=as.numeric(Signal), col=time)) +
geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F ) +
scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
labs(
x = "",
y = "\n Log normalized \n "
) +
scale_x_discrete()
Warning message: "Transformation introduced infinite values in continuous y-axis" Warning message: "Removed 2 rows containing non-finite values (stat_ydensity)."
#Wilcox test
wilcox.test(filtered_0h, filtered_1h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)
wilcox.test(filtered_0h, filtered_4h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)
Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, : "cannot compute exact p-value with ties" Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, : "cannot compute exact confidence intervals with ties"
Wilcoxon rank sum test with continuity correction
data: filtered_0h and filtered_1h
W = 8.6175e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
3.852630e-05 3.044874e-05
sample estimates:
difference in location
4.329485e-05
Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, : "cannot compute exact p-value with ties" Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, : "cannot compute exact confidence intervals with ties"
Wilcoxon rank sum test with continuity correction
data: filtered_0h and filtered_4h
W = 7.3154e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
-1.839428e-05 -4.791938e-05
sample estimates:
difference in location
-6.576012e-05
wilcox.test(filtered_1h, filtered_4h, mu = 0, paired=F, alternative = "two.sided", exact=T)
Warning message in wilcox.test.default(filtered_1h, filtered_4h, mu = 0, paired = F, : "cannot compute exact p-value with ties"
Wilcoxon rank sum test with continuity correction data: filtered_1h and filtered_4h W = 6.0277e+10, p-value < 2.2e-16 alternative hypothesis: true location shift is not equal to 0
Draw Violin plots to show the distribution of normalized H3K4me3 signal at enhancers¶mark_violin = tibble(
R1_0h=rowSums(filtered_0h),
R1_1h=rowSums(filtered_1h),
R1_4h=rowSums(filtered_4h),
ID = 1:length(R1_0h)
) %>%
pivot_longer( R1_0h:R1_4h, names_to = "Sample", values_to = "Signal" ) %>%
#substr = select from column "Sample" at start=2, end=2
mutate( Rep=substr(Sample, 2, 2), time=substr(Sample, 4, 5) );
ggplot(mark_violin, aes(x=paste0(time, " "), y=as.numeric(Signal), col=time)) +
geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F ) +
scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
labs(
x = "",
y = "\n Relative signal "
) +
scale_x_discrete()
Warning message: "Transformation introduced infinite values in continuous y-axis" Warning message: "Removed 2 rows containing non-finite values (stat_ydensity)."
#Wilcox test
wilcox.test(filtered_0h, filtered_1h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)
wilcox.test(filtered_0h, filtered_4h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)
Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, : "cannot compute exact p-value with ties" Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, : "cannot compute exact confidence intervals with ties"
Wilcoxon rank sum test with continuity correction
data: filtered_0h and filtered_1h
W = 8.6175e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
3.852630e-05 3.044874e-05
sample estimates:
difference in location
4.329485e-05
Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, : "cannot compute exact p-value with ties" Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, : "cannot compute exact confidence intervals with ties"
Wilcoxon rank sum test with continuity correction
data: filtered_0h and filtered_4h
W = 7.3154e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
-1.839428e-05 -4.791938e-05
sample estimates:
difference in location
-6.576012e-05
</center>
#Import coordinates of promoters that lost H3K4me1
K4me1.loss = read.table("../K4me1/GenePromoters_ThatLose.K4me1.bed");
colnames(K4me1.loss) = c("chr", "start", "end", "width", "log2FC_10");
K4me1.loss = makeGRangesFromDataFrame(K4me1.loss);
K4me1.loss = resize(K4me1.loss, width = 4000, fix = "start");
#K4me1.loss = promoters(K4me1.loss, upstream=0, downstream=2000);
K4me1.loss
GRanges object with 430 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] \303chr2 122286456-122290455 *
[2] chr1 25553946-25557945 *
[3] chr19 49373678-49377677 *
[4] chr1 109640815-109644814 *
[5] chr9 127983623-127987622 *
... ... ... ...
[426] chr15 40381114-40385113 *
[427] chr15 43510973-43514972 *
[428] chr3 39214085-39218084 *
[429] chr12 52279888-52283887 *
[430] chr16 2519481-2523480 *
-------
seqinfo: 23 sequences from an unspecified genome; no seqlengths
#4. Experimental H3K36me3 signal in regions of interest
K4me3_0h_br1.perBin = Count.reads.InBins(K4me3_0h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
K4me3_1h_br1.perBin = Count.reads.InBins(K4me3_1h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
K4me3_4h_br1.perBin = Count.reads.InBins(K4me3_4h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
K4me3_0h_br2.perBin = Count.reads.InBins(K4me3_0h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
K4me3_1h_br2.perBin = Count.reads.InBins(K4me3_1h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
K4me3_4h_br2.perBin = Count.reads.InBins(K4me3_4h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, 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HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, 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HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"
#5. WCE reads in regions of interest
WCE.K27ac_0h_br1.perBin = Count.reads.InBins(WCE_0h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
WCE.K27ac_1h_br1.perBin = Count.reads.InBins(WCE_1h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
WCE.K27ac_4h_br1.perBin = Count.reads.InBins(WCE_4h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
WCE.K27ac_0h_br2.perBin = Count.reads.InBins(WCE_0h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
WCE.K27ac_1h_br2.perBin = Count.reads.InBins(WCE_1h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
WCE.K27ac_4h_br2.perBin = Count.reads.InBins(WCE_4h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s" Warning message in .Seqinfo.mergexy(x, y): "Each of the 2 combined objects has sequence levels not in the other: - in 'x': <c3>chr2 - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"
#6. Calculate theotic value from the linear regressions and the WCE reads per Bin
K4me3_0h_br1.theoretic.perBin = (0.96111 * WCE.K27ac_0h_br1.perBin) + 27.42451;
K4me3_1h_br1.theoretic.perBin = (0.11971 * WCE.K27ac_1h_br1.perBin) + 6.64561;
K4me3_4h_br1.theoretic.perBin = (0.44505 * WCE.K27ac_4h_br1.perBin) + 12.22014;
K4me3_0h_br2.theoretic.perBin = (0.34377 * WCE.K27ac_0h_br2.perBin) + 13.10884;
K4me3_1h_br2.theoretic.perBin = (0.25230 * WCE.K27ac_1h_br2.perBin) + 10.46680;
K4me3_4h_br2.theoretic.perBin = (0.21612 * WCE.K27ac_4h_br2.perBin) + 3.01524;
#7. Calculate the residuals
res_0h_br1 = K4me3_0h_br1.perBin - K4me3_0h_br1.theoretic.perBin;
res_1h_br1 = K4me3_1h_br1.perBin - K4me3_1h_br1.theoretic.perBin;
res_4h_br1 = K4me3_4h_br1.perBin - K4me3_4h_br1.theoretic.perBin;
res_0h_br2 = K4me3_0h_br2.perBin - K4me3_0h_br2.theoretic.perBin;
res_1h_br2 = K4me3_1h_br2.perBin - K4me3_1h_br2.theoretic.perBin;
res_4h_br2 = K4me3_4h_br2.perBin - K4me3_4h_br2.theoretic.perBin;
#8. Replace all residuals < 0 with 0
res_0h_br1[res_0h_br1 < 0] = 0;
res_1h_br1[res_1h_br1 < 0] = 0;
res_4h_br1[res_4h_br1 < 0] = 0;
res_0h_br2[res_0h_br2 < 0] = 0;
res_1h_br2[res_1h_br2 < 0] = 0;
res_4h_br2[res_4h_br2 < 0] = 0;
#9. Keep only the entries were both replicates have reads
badgenes_0h = which(rowSums(res_0h_br1)<1 | rowSums(res_0h_br2)<1 | rowSums(res_1h_br1)<1 | rowSums(res_1h_br2)<1 | rowSums(res_4h_br1)<1 | rowSums(res_4h_br2)<1);
filtered_0h_br1 = res_0h_br1[-badgenes_0h,];
filtered_0h_br2 = res_0h_br2[-badgenes_0h,];
#1h
filtered_1h_br1 = res_1h_br1[-badgenes_0h,];
filtered_1h_br2 = res_1h_br2[-badgenes_0h,];
#4h
filtered_4h_br1 = res_4h_br1[-badgenes_0h,];
filtered_4h_br2 = res_4h_br2[-badgenes_0h,];
length(filtered_0h_br1)
#1. Average normalized replicates
filtered_0h = ((res_0h_br1 /2530) + (res_0h_br2 /346))/2;
filtered_1h = ((res_1h_br1 /3048) + (res_1h_br2 /1724))/2;
filtered_4h = ((res_4h_br1 /4108) + (res_4h_br2 /1782))/2;
#9. Subsample residual matrices and plot metaplots
res_0h.subs = metaSubsampleMatrix(filtered_0h);
res_1h.subs = metaSubsampleMatrix(filtered_1h);
res_4h.subs = metaSubsampleMatrix(filtered_4h);
#10. Give miningful names to each dataset --> thse names will be used as labels for the plot
res_0h.subs$sample.name = "0h ";
res_1h.subs$sample.name = "1h ";
res_4h.subs$sample.name = "4h ";
theme_set(
theme_classic() +
theme(
panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=0.5),
panel.grid.major = element_line(colour = "white"),
axis.text.x = element_text( color="black", size=14),
axis.text.y = element_text( color="black", size=16),
axis.title.x = element_text(color="black", size=14),
axis.title.y = element_text(color="black", size=16)
)
);
#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles ---> RPM norm data
# --> Enhancers
options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=3, repr.plot.height=2);
plot.merged = rbind(res_0h.subs, res_1h.subs, res_4h.subs);
ggplot(plot.merged, aes(x=x, y=mean, color=sample.name)) +
geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
#scale_colour_manual(values = c("#005ab3", "#ff8da1", "#ff6500")) +
scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
scale_y_continuous(labels = c(0, 2, 4), breaks=c(0.00, 0.02, 0.04)) +
scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
labs(
x = " Distance to TSS [kb]",
y = "Normalized \n signal "
)
</center>
#Import H3 Cut&Run Bam files:
##0h Trp
load("/home/danko_0001/projects/RawSequenceFiles/2019-11-06_K562_TrpATACseq_TrpCutRun/CutandRun_antiH3/align_hg19SacCer1/11283_11142_109460_HKLV3BGXC_CutRun_Cut_Run_0h_TAGCTT.Rdata");
CR0 = reads;
rm(reads);
##1h Trp
a = load("/home/danko_0001/projects/RawSequenceFiles/2019-11-06_K562_TrpATACseq_TrpCutRun/CutandRun_antiH3/align_hg19SacCer1/11283_11142_109460_HKLV3BGXC_CutRun_Cut_Run_1h_AGTTCC.Rdata");
CR1 = reads;
rm(reads);
##4h Trp
a = load("/home/danko_0001/projects/RawSequenceFiles/2019-11-06_K562_TrpATACseq_TrpCutRun/CutandRun_antiH3/align_hg19SacCer1/11283_11142_109460_HKLV3BGXC_CutRun_Cut_Run_4h_CCGTCC.Rdata");
CR4 = reads;
rm(reads);
#Subset each GRanges to nly have mono-nuc fragments
CR0_mono = CR0[width(CR0) >= 120 & width(CR0) < 180];
CR1_mono = CR1[width(CR1) >= 120 & width(CR1) < 180];
CR4_mono = CR4[width(CR4) >= 120 & width(CR4) < 180];
CR0_norm = CR0_mono;
CR1_norm = CR1_mono;
CR4_norm = CR4_mono;
#Correct the Cut&Run daa using spike-ins
#Multiply each BigWig by these normalization factors
CR0_norm$score = CR0_mono$count * 1;
CR1_norm$score = CR1_mono$count * 1.300083224;
CR4_norm$score = CR4_mono$count * 1.257619321;
#Overlap maxTSS with each mono-nucleosome Granges
CR_p_0 = Count.reads.InBins(CR0_norm, promoters.maxTSS, spike = 1, binsize = 100, field = "score");
CR_p_1 = Count.reads.InBins(CR1_norm, promoters.maxTSS, spike = 1, binsize = 100, field = "score");
CR_p_4 = Count.reads.InBins(CR4_norm, promoters.maxTSS, spike = 1, binsize = 100, field = "score");
#Make matrix to run limma
scatter = tibble(
K4me3_0h = (rowSums(res_0h_br1) + rowSums(res_0h_br2))/2,
K4me3_1h = (rowSums(res_1h_br1) + rowSums(res_1h_br2))/2,
K4me3_4h = (rowSums(res_4h_br1) + rowSums(res_4h_br2))/2,
H3_0h = rowSums(CR_p_0),
H3_1h = rowSums(CR_p_1),
H3_4h = rowSums(CR_p_4)
);
head(scatter)
| K4me3_0h | K4me3_1h | K4me3_4h | H3_0h | H3_1h | H3_4h |
|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> |
| 1432.85370 | 419.49468 | 857.29656 | 10 | 12 | 5 |
| 49.59815 | 12.34270 | 85.60742 | 17 | 7 | 2 |
| 1014.51597 | 250.17208 | 602.80796 | 11 | 3 | 2 |
| 937.35234 | 342.03511 | 589.53700 | 13 | 8 | 4 |
| 706.23136 | 212.06016 | 480.43168 | 6 | 8 | 5 |
| 93.13324 | 19.15575 | 135.67336 | 3 | 8 | 1 |
scatter.filt = scatter[scatter$K4me3_0h > 1, ];
scatter.filt = scatter.filt[scatter.filt$K4me3_1h > 1, ];
scatter.filt = scatter.filt[scatter.filt$K4me3_4h > 1, ];
cor.test(scatter.filt$K4me3_0h, scatter.filt$H3_0h, method="spearman");
cor.test(scatter.filt$K4me3_0h, scatter.filt$H3_0h, method="pearson");
Spearman's rank correlation rho
data: scatter.filt$K4me3_0h and scatter.filt$H3_0h
S = 1.4108e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.2374296
Pearson's product-moment correlation
data: scatter.filt$K4me3_0h and scatter.filt$H3_0h
t = 38.242, df = 10352, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.3348367 0.3685937
sample estimates:
cor
0.3518296
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_0h, H3_0h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 versus H3 \n S = 0.2374296, P = 0.3518296 \n",
x = "H3K4me3 0h",
y = "H3 0h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
cor.test(scatter.filt$K4me3_1h, scatter.filt$H3_1h, method="spearman");
cor.test(scatter.filt$K4me3_1h, scatter.filt$H3_1h, method="pearson");
Spearman's rank correlation rho
data: scatter.filt$K4me3_1h and scatter.filt$H3_1h
S = 1.3572e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.2663835
Pearson's product-moment correlation
data: scatter.filt$K4me3_1h and scatter.filt$H3_1h
t = 39.458, df = 10352, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.3447102 0.3781996
sample estimates:
cor
0.3615715
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_1h, H3_1h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 versus H3 \n S = 0.2663835, P = 0.3615715 \n",
x = "H3K4me3 1h",
y = "H3 1h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
cor.test(scatter.filt$K4me3_4h, scatter.filt$H3_4h, method="spearman");
cor.test(scatter.filt$K4me3_4h, scatter.filt$H3_4h, method="pearson");
Spearman's rank correlation rho
data: scatter.filt$K4me3_4h and scatter.filt$H3_4h
S = 1.3452e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.27287
Pearson's product-moment correlation
data: scatter.filt$K4me3_4h and scatter.filt$H3_4h
t = 35.502, df = 10352, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.3121743 0.3465185
sample estimates:
cor
0.3294554
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_4h, H3_4h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
#scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 versus H3 \n S = 0.27287, P = 0.3294554 \n",
x = "H3K4me3 4h",
y = "H3 4h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
# Compute log2FC
K4me3.log2FC = log2(scatter.filt$K4me3_4h / scatter.filt$K4me3_0h);
H3.log2FC = log2(scatter.filt$H3_4h / scatter.filt$H3_0h);
# Merge
K4me3_H3_log2FC = cbind(K4me3.log2FC, H3.log2FC);
colnames(K4me3_H3_log2FC) = c("K4me3_04", "H3_04");
K4me3_H3_log2FC = as.data.frame(K4me3_H3_log2FC);
# Remove TSS with infinite values
K4me3_H3_log2FC = K4me3_H3_log2FC[is.finite(rowSums(K4me3_H3_log2FC)),];
#9665
K4me3_H3_log2FC[K4me3_H3_log2FC$K4me3_04 < 0, ]
| K4me3_04 | H3_04 | |
|---|---|---|
| <dbl> | <dbl> | |
| 1 | -0.741025053 | -1.0000000 |
| 3 | -0.751021196 | -2.4594316 |
| 4 | -0.669009086 | -1.7004397 |
| 5 | -0.555809598 | -0.2630344 |
| 7 | -0.395517186 | -0.3219281 |
| 8 | -0.756926005 | -1.5849625 |
| 9 | -0.411062579 | -1.7004397 |
| 11 | -0.871135078 | 0.0000000 |
| 13 | -0.470624297 | -0.7369656 |
| 14 | -0.301230654 | -2.0000000 |
| 15 | -0.402705062 | -0.1926451 |
| 16 | -0.780737230 | -0.7776076 |
| 17 | -0.715910704 | -1.7004397 |
| 19 | -0.494697097 | -0.8073549 |
| 21 | -0.346029041 | 0.2223924 |
| 22 | -0.162221096 | -1.5849625 |
| 24 | -0.769150443 | 0.1375035 |
| 25 | -0.205658073 | -1.5849625 |
| 26 | -0.370000967 | -1.0995357 |
| 28 | -0.289582560 | -1.0000000 |
| 29 | -0.013566602 | -0.3625701 |
| 30 | -0.444844892 | 0.0000000 |
| 31 | -0.769813609 | -0.1375035 |
| 32 | -0.258388130 | -0.8930848 |
| 33 | -0.513039769 | -1.8073549 |
| 35 | -0.542113550 | -1.5849625 |
| 38 | -0.005449026 | -2.0000000 |
| 40 | -0.349569965 | -1.5025003 |
| 42 | -0.401339532 | 0.8930848 |
| 43 | -0.177187356 | -1.0000000 |
| ⋮ | ⋮ | ⋮ |
| 10229 | -0.82938601 | -1.8744691 |
| 10230 | -0.09212628 | 0.5849625 |
| 10231 | -0.55135746 | -0.8744691 |
| 10232 | -0.47920494 | -2.0000000 |
| 10235 | -0.46219911 | 1.0780025 |
| 10236 | -0.85984331 | 0.5849625 |
| 10248 | -0.47706927 | -0.8479969 |
| 10255 | -0.35782993 | 0.4854268 |
| 10259 | -0.20352585 | -2.1699250 |
| 10271 | -0.21971021 | 0.5849625 |
| 10273 | -0.20820714 | -1.3219281 |
| 10274 | -0.03795069 | -2.4594316 |
| 10280 | -0.70293520 | -1.7369656 |
| 10287 | -0.26645931 | -1.7369656 |
| 10291 | -0.10390801 | -0.8479969 |
| 10294 | -0.23326875 | 0.5849625 |
| 10303 | -0.09632808 | -0.5849625 |
| 10313 | -0.57879898 | -0.2223924 |
| 10315 | -0.13093482 | -2.0000000 |
| 10316 | -0.18300941 | -1.5849625 |
| 10317 | -1.07910737 | -1.2630344 |
| 10318 | -0.37029795 | -0.7369656 |
| 10319 | -0.58640658 | -1.4150375 |
| 10325 | -0.18997347 | 1.4150375 |
| 10329 | -0.81454761 | -0.8073549 |
| 10330 | -0.33945775 | -2.5849625 |
| 10337 | -0.43178048 | 2.0000000 |
| 10338 | -0.34762096 | -0.4854268 |
| 10340 | -0.36501301 | -2.3219281 |
| 10345 | -0.49992393 | 0.0000000 |
cor.test(K4me3_H3_log2FC$K4me3_04, K4me3_H3_log2FC$H3_04, method="spearman");
cor.test(K4me3_H3_log2FC$K4me3_04, K4me3_H3_log2FC$H3_04, method="pearson");
Spearman's rank correlation rho
data: K4me3_H3_log2FC$K4me3_04 and K4me3_H3_log2FC$H3_04
S = 1.7271e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.1477697
Pearson's product-moment correlation
data: K4me3_H3_log2FC$K4me3_04 and K4me3_H3_log2FC$H3_04
t = -12.515, df = 9663, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.1458644 -0.1066264
sample estimates:
cor
-0.1262948
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(K4me3_H3_log2FC), mapping=aes(K4me3_04, H3_04)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4, slope = -1) +
#scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 versus H3 \n S = -0.1477697, P = -0.1262948 \n",
x = "H3K4me3 4h/0h",
y = "H3 4h/0h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
# Compute log2FC
K4me3.log2FC_01 = log2(scatter.filt$K4me3_1h / scatter.filt$K4me3_0h);
H3.log2FC_01 = log2(scatter.filt$H3_1h / scatter.filt$H3_0h);
# Merge
K4me3_H3_log2FC_01 = cbind(K4me3.log2FC_01, H3.log2FC_01);
colnames(K4me3_H3_log2FC_01) = c("K4me3_01", "H3_01");
K4me3_H3_log2FC_01 = as.data.frame(K4me3_H3_log2FC_01);
# Remove TSS with infinite values
K4me3_H3_log2FC_01 = K4me3_H3_log2FC_01[is.finite(rowSums(K4me3_H3_log2FC_01)),];
cor.test(K4me3_H3_log2FC_01$K4me3_01, K4me3_H3_log2FC_01$H3_01, method="spearman");
cor.test(K4me3_H3_log2FC_01$K4me3_01, K4me3_H3_log2FC_01$H3_01, method="pearson");
Spearman's rank correlation rho
data: K4me3_H3_log2FC_01$K4me3_01 and K4me3_H3_log2FC_01$H3_01
S = 1.8168e+11, p-value = 1.794e-06
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.04741578
Pearson's product-moment correlation
data: K4me3_H3_log2FC_01$K4me3_01 and K4me3_H3_log2FC_01$H3_01
t = -5.8132, df = 10132, p-value = 6.313e-09
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.07703986 -0.03822916
sample estimates:
cor
-0.05765629
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(K4me3_H3_log2FC), mapping=aes(K4me3_04, H3_04)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4, slope = -1) +
#scale_x_log10() + scale_y_log10() +
labs(
title = "\n H3K4me3 versus H3 \n S = -0.04741578, P = -0.05765629 \n",
x = "H3K4me3 1h/0h",
y = "H3 1h/0h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
</center>
#Import PROseq BigWigs
PROseq_0h_plus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_0h_plus_normalized_NateWay.bw");
PROseq_1h_plus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_1h_plus_normalized_NateWay.bw");
PROseq_4h_plus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_4h_plus_normalized_NateWay.bw");
PROseq_0h_minus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_0h_minus_normalized_NateWay.bw");
PROseq_1h_minus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_1h_minus_normalized_NateWay.bw");
PROseq_4h_minus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_4h_minus_normalized_NateWay.bw");
#Set strand manually
strand(PROseq_0h_plus) = "+";
strand(PROseq_1h_plus) = "+";
strand(PROseq_4h_plus) = "+";
strand(PROseq_0h_minus) = "-";
strand(PROseq_1h_minus) = "-";
strand(PROseq_4h_minus) = "-";
#Merge PROseq per time point
PROseq_0h = append(PROseq_0h_plus, PROseq_0h_minus);
PROseq_1h = append(PROseq_1h_plus, PROseq_1h_minus);
PROseq_4h = append(PROseq_4h_plus, PROseq_4h_minus);
#Normalize PROseq data by dividing with the total number of spike-in reads in each sample:
# --> score = not normalized reads
# --> count = normalized reads
PROseq_0h$count = PROseq_0h$score * 1/1;
PROseq_1h$count = PROseq_1h$score * 1/1;
PROseq_4h$count = PROseq_4h$score * 1/1;
#1. Import gene coordinates in hg19
genes=read.table("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/gencode.v19.annotation.gtf.gz", header=F, stringsAsFactors=F);
colnames(genes) = c("chr", "Transcript", "start", "end", "strand", "gene_id", "transcript_id", "gene_type", "gene_name", "TranscriptName");
genes = genes[genes$Transcript =="transcript",];
genes = as(genes, "GRanges");
#Order genes based on their length
genes = genes[order(width(genes))];
genes = genes[!duplicated(genes$gene_name)];
genes = genes[width(genes) > 250];
#genes_resize = promoters(genes, upstream=2000, downstream=2000);
#Get separate coordinates for pause site and GB
#GB
promoters.GB.coord = genebodies(genes, start = 200, end = -200, fix.start = "start", fix.end = "end");
#Start-to-pause coordinates
promoters.Pause.coord = genebodies(genes, start = 0, end = 200, fix.start = "start", fix.end = "start");
#Compute coverage of the Rdata provided as hist.mark
PROseq_0h = makeGRangesBRG(PROseq_0h);
PROseq_1h = makeGRangesBRG(PROseq_1h);
PROseq_4h = makeGRangesBRG(PROseq_4h);
#Count hist.mark signal per GB
PROseq.0h_GB = getCountsByRegions(PROseq_0h, promoters.GB.coord, field = "count");
PROseq.1h_GB = getCountsByRegions(PROseq_1h, promoters.GB.coord, field = "count");
PROseq.4h_GB = getCountsByRegions(PROseq_4h, promoters.GB.coord, field = "count");
#Count hist.mark signal per Pause
PROseq.0h_Pause = getCountsByRegions(PROseq_0h, promoters.Pause.coord, field = "count");
PROseq.1h_Pause = getCountsByRegions(PROseq_1h, promoters.Pause.coord, field = "count");
PROseq.4h_Pause = getCountsByRegions(PROseq_4h, promoters.Pause.coord, field = "count");
#Get H3K4me3 signal per gene and average normalized replicates
filtered_0h = ((res_0h_br1 /2530) + (res_0h_br2 /346))/2;
filtered_1h = ((res_1h_br1 /3048) + (res_1h_br2 /1724))/2;
filtered_4h = ((res_4h_br1 /4108) + (res_4h_br2 /1782))/2;
write.table(rowSums(filtered_0h), "./H3K4me3.0h_SignalPerGeneLarger250bp.bed", quote=F, sep="\t", row.names=F, col.names=F);
write.table(rowSums(filtered_4h), "./H3K4me3.4h_SignalPerGeneLarger250bp.bed", quote=F, sep="\t", row.names=F, col.names=F);
#Make matrix to run limma
scatter = tibble(
PROseq.GB_0h = abs(PROseq.0h_GB),
PROseq.GB_1h = abs(PROseq.1h_GB),
PROseq.GB_4h = abs(PROseq.4h_GB),
PROseq.Pause_0h = abs(PROseq.0h_Pause),
PROseq.Pause_1h = abs(PROseq.1h_Pause),
PROseq.Pause_4h = abs(PROseq.4h_Pause),
K4me3_0h = rowSums(filtered_0h),
K4me3_1h = rowSums(filtered_1h),
K4me3_4h = rowSums(filtered_4h)
);
head(scatter)
| PROseq.GB_0h | PROseq.GB_1h | PROseq.GB_4h | PROseq.Pause_0h | PROseq.Pause_1h | PROseq.Pause_4h | K4me3_0h | K4me3_1h | K4me3_4h |
|---|---|---|---|---|---|---|---|---|
| <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> |
| 0 | 0.000000 | 0 | 0 | 0.000000 | 0.000000 | 0.0000000 | 0.00000000 | 0.00000000 |
| 0 | 0.000000 | 0 | 0 | 0.000000 | 0.000000 | 0.0000000 | 0.00000000 | 0.00000000 |
| 0 | 2.787623 | 0 | 5 | 4.181434 | 4.085787 | 0.1870537 | 0.01757447 | 0.05522856 |
| 0 | 0.000000 | 0 | 0 | 0.000000 | 0.000000 | 0.0000000 | 0.00000000 | 0.00000000 |
| 0 | 0.000000 | 0 | 0 | 0.000000 | 0.000000 | 0.0000000 | 0.00000000 | 0.00000000 |
| 0 | 0.000000 | 0 | 0 | 0.000000 | 0.000000 | 0.0000000 | 0.00000000 | 0.00000000 |
scatter.filt = scatter[scatter$PROseq.GB_0h > 0, ];
scatter.filt = scatter.filt[scatter.filt$PROseq.GB_1h > 0, ];
scatter.filt = scatter.filt[scatter.filt$PROseq.GB_4h > 0, ];
cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.GB_0h, method="spearman");
cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.GB_0h, method="pearson");
Spearman's rank correlation rho
data: scatter.filt$K4me3_0h and scatter.filt$PROseq.GB_0h
S = 3.7282e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.5536334
Pearson's product-moment correlation
data: scatter.filt$K4me3_0h and scatter.filt$PROseq.GB_0h
t = 34.144, df = 7941, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.3384605 0.3768166
sample estimates:
cor
0.3577895
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.GB_0h, K4me3_0h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
#geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.5479982, P = 0.3887045 \n",
y = "H3K4me3 0h",
x = "PROseq - GeneBody 0h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_1h, PROseq.GB_1h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.421042, P = 0.2597497 \n",
x = "H3K4me3 1h",
y = "PROseq - GeneBody 1h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_4h, PROseq.GB_4h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.1946126, P = 0.08440513 \n",
x = "H3K4me3 4h",
y = "PROseq - GeneBody 4h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.Pause_0h, method="spearman");
cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.Pause_0h, method="pearson");
Spearman's rank correlation rho
data: scatter.filt$K4me3_0h and scatter.filt$PROseq.Pause_0h
S = 2.5431e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.6955184
Pearson's product-moment correlation
data: scatter.filt$K4me3_0h and scatter.filt$PROseq.Pause_0h
t = 47.191, df = 7941, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.4506386 0.4849932
sample estimates:
cor
0.4679927
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.Pause_0h, K4me3_0h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
#geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.6901721, P = 0.4765192 \n",
y = "H3K4me3 0h",
x = "PROseq - Pause 0h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.Pause_1h, K4me3_1h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.5891095, P = 0.5099145 \n",
y = "H3K4me3 1h",
x = "PROseq - Pause 1h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.Pause_4h, K4me3_4h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.3589597, P = 0.2611949 \n",
y = "H3K4me3 4h",
x = "PROseq - Pause 4h"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
</center>
#Make matrix to run limma
scatter.log2FC = tibble(
PROseq.GB_04h = log2(abs(PROseq.4h_GB)/(abs(PROseq.0h_GB)+1)),
PROseq.Pause_04h = log2(abs(PROseq.4h_Pause)/(abs(PROseq.0h_Pause)+1)),
K4me3_04h = log2((rowSums(filtered_4h))/(rowSums(filtered_0h)+1))
);
scatter.log2FC = scatter.log2FC[is.finite(rowSums(scatter.log2FC)),];
#scatter.log2FC = scatter.log2FC[scatter.log2FC$K4me3_04h > -5, ];
cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.GB_04h, method="spearman");
cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.GB_04h, method="pearson");
Spearman's rank correlation rho
data: scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.GB_04h
S = 852409639, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.4140822
Pearson's product-moment correlation
data: scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.GB_04h
t = -22.913, df = 1533, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.5414324 -0.4668465
sample estimates:
cor
-0.5050819
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.log2FC), mapping=aes(PROseq.GB_04h, K4me3_04h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
#geom_abline(alpha=0.4) +
#scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.3302053, P = 0.4100412 \n",
y = "H3K4me3 log2(0h/4h)",
x = "PROseq - GebeBody log2(0h/4h)"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.Pause_04h, method="spearman");
cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.Pause_04h, method="pearson");
Spearman's rank correlation rho
data: scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.Pause_04h
S = 669210733, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.3876175
Pearson's product-moment correlation
data: scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.Pause_04h
t = -19.296, df = 1423, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.4956075 -0.4132428
sample estimates:
cor
-0.4553991
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.log2FC), mapping=aes(PROseq.Pause_04h, K4me3_04h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
#geom_abline(alpha=0.4) +
#scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.4255293, P = 0.6121219 \n",
y = "H3K4me3 log2(0h/4h)",
x = "PROseq - Pause log2(0h/4h)"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
</center>
*Pause Index = Pause.signal/GB.signal
#Make matrix to run limma
scatter.PauseIndex = tibble(
PROseq.0h_PI = abs(PROseq.0h_Pause)/(abs(PROseq.0h_GB)),
PROseq.1h_PI = abs(PROseq.1h_Pause)/(abs(PROseq.1h_GB)),
PROseq.4h_PI = abs(PROseq.4h_Pause)/(abs(PROseq.4h_GB)),
K4me3.0h_PI = rowSums(filtered_0h),
K4me3.1h_PI = rowSums(filtered_1h),
K4me3.4h_PI = rowSums(filtered_4h)
);
scatter.PauseIndex = scatter.PauseIndex[is.finite(rowSums(scatter.PauseIndex)),];
cor.test(scatter.PauseIndex$K4me3.0h_PI, scatter.PauseIndex$PROseq.0h_PI, method="spearman");
cor.test(scatter.PauseIndex$K4me3.0h_PI, scatter.PauseIndex$PROseq.0h_PI, method="pearson");
Spearman's rank correlation rho
data: scatter.PauseIndex$K4me3.0h_PI and scatter.PauseIndex$PROseq.0h_PI
S = 4.1583e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.5021315
Pearson's product-moment correlation
data: scatter.PauseIndex$K4me3.0h_PI and scatter.PauseIndex$PROseq.0h_PI
t = 16.403, df = 7941, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.1596727 0.2022163
sample estimates:
cor
0.1810292
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.PauseIndex), mapping=aes(PROseq.0h_PI, K4me3.0h_PI)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
geom_abline(alpha=0.4) +
scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.4968961, P = 0.1933199 \n",
y = "H3K4me3 0h",
x = "PROseq 0h - PauseIndex"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)
cor.test(scatter.PauseIndex$K4me3.1h_PI, scatter.PauseIndex$PROseq.1h_PI, method="spearman");
cor.test(scatter.PauseIndex$K4me3.1h_PI, scatter.PauseIndex$PROseq.1h_PI, method="pearson");
Spearman's rank correlation rho
data: scatter.PauseIndex$K4me3.1h_PI and scatter.PauseIndex$PROseq.1h_PI
S = 6.523e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.4670988
Pearson's product-moment correlation
data: scatter.PauseIndex$K4me3.1h_PI and scatter.PauseIndex$PROseq.1h_PI
t = 21.484, df = 19436, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.1385459 0.1660101
sample estimates:
cor
0.1523074
cor.test(scatter.PauseIndex$K4me3.4h_PI, scatter.PauseIndex$PROseq.4h_PI, method="spearman");
cor.test(scatter.PauseIndex$K4me3.4h_PI, scatter.PauseIndex$PROseq.4h_PI, method="pearson");
Spearman's rank correlation rho
data: scatter.PauseIndex$K4me3.4h_PI and scatter.PauseIndex$PROseq.4h_PI
S = 8.6453e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.2937223
Pearson's product-moment correlation
data: scatter.PauseIndex$K4me3.4h_PI and scatter.PauseIndex$PROseq.4h_PI
t = 9.2811, df = 19436, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.05241662 0.08040883
sample estimates:
cor
0.0664258
</center>
*Pause Index = Pause.signal/GB.signal
#Make matrix to run limma
scatter.log2FC.PI = tibble(
PROseq.04h_PI = log2( abs(PROseq.4h_Pause)/abs(PROseq.4h_GB) / (abs(PROseq.0h_Pause)/(abs(PROseq.0h_GB))) ),
K4me3_04h = log2( ((rowSums(filtered_4h)+1) ) / (rowSums(filtered_0h)+1) )
);
scatter.log2FC.PI = scatter.log2FC.PI[is.finite(rowSums(scatter.log2FC.PI)),];
#scatter.log2FC.PI = scatter.log2FC.PI[scatter.log2FC.PI$K4me3_04h < 0, ];
cor.test(scatter.log2FC.PI$K4me3_04h, scatter.log2FC.PI$PROseq.04h_PI, method="spearman");
cor.test(scatter.log2FC.PI$K4me3_04h, scatter.log2FC.PI$PROseq.04h_PI, method="pearson");
Spearman's rank correlation rho
data: scatter.log2FC.PI$K4me3_04h and scatter.log2FC.PI$PROseq.04h_PI
S = 1134619808, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
0.3282156
Pearson's product-moment correlation
data: scatter.log2FC.PI$K4me3_04h and scatter.log2FC.PI$PROseq.04h_PI
t = 14.26, df = 2162, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.2542082 0.3312490
sample estimates:
cor
0.2932045
options(warn=-1)
options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);
ggplot(as.data.frame(scatter.log2FC.PI), mapping=aes(PROseq.04h_PI, K4me3_04h)) + geom_point() +
#The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
#where adjust = 0.5 means use half of the default bandwidth.
geom_pointdensity(adjust = 10, size = 2) +
scale_color_viridis()+
#geom_abline(alpha=0.4) +
#scale_x_log10() + scale_y_log10() +
labs(
title = "\n S = 0.3282156, P = 0.2932045 \n",
y = "H3K4me3 log2(4h/0h)",
x = "PROseq - PauseIndex log2(4h/0h)"
) +
theme_classic() +
theme(
#panel.border = element_blank(),
# Remove panel background
panel.background = element_blank(),
legend.background = element_blank(),
# Add axis line
axis.line = element_line(colour = "black", size=1),
panel.grid.major = element_line(colour = "white"),
plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
)